median 0.0 0.1 0.2 0.3 0.4 6 8 10 log(intensity) density sample 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 Intensity distribution over all samples Save figure
6 8 10 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 log(intensity) Intensity distribution in each sample Save figure


10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 0.95 0.96 0.97 0.98 0.99 1.00 Coefficient Sample correlation Save figure
0 1000 2000 3000 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 count By matching By MS/MS Identification types distribution accross samples Save figure


-10 -5 0 5 10amol_1_ratio_5fmol_4 10amol_2_ratio_5fmol_4 10amol_3_ratio_5fmol_4 10amol_4_ratio_5fmol_4 50amol_1_ratio_5fmol_4 50amol_3_ratio_5fmol_4 50amol_2_ratio_5fmol_4 50amol_4_ratio_5fmol_4 100amol_1_ratio_5fmol_4 100amol_3_ratio_5fmol_4 100amol_2_ratio_5fmol_4 100amol_4_ratio_5fmol_4 250amol_1_ratio_5fmol_4 250amol_2_ratio_5fmol_4 250amol_3_ratio_5fmol_4 250amol_4_ratio_5fmol_4 500amol_1_ratio_5fmol_4 500amol_3_ratio_5fmol_4 500amol_2_ratio_5fmol_4 500amol_4_ratio_5fmol_4 1fmol_1_ratio_5fmol_4 1fmol_2_ratio_5fmol_4 1fmol_3_ratio_5fmol_4 1fmol_4_ratio_5fmol_4 5fmol_1_ratio_5fmol_4 5fmol_3_ratio_5fmol_4 5fmol_2_ratio_5fmol_4 10fmol_1_ratio_5fmol_4 10fmol_2_ratio_5fmol_4 10fmol_3_ratio_5fmol_4 10fmol_4_ratio_5fmol_4 25fmol_1_ratio_5fmol_4 25fmol_2_ratio_5fmol_4 25fmol_3_ratio_5fmol_4 25fmol_4_ratio_5fmol_4 50fmol_1_ratio_5fmol_4 50fmol_2_ratio_5fmol_4 50fmol_3_ratio_5fmol_4 50fmol_4_ratio_5fmol_4 log2(ratio) Ratio distribution for each sample Save figure


0.0 0.1 0.2 0.3 0.4 6 8 10 intensity density sample 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 Intensity distribution over all samples after normalization Save figure
6 8 10 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 log10(intensity) Intensity distribution in each sample after normalization Save figure


Normalization method : each intensity is expressed relatively to a reference intensity, as a ratio of intensities. Intensities of the sample with the lowest number of missing values are used as reference intensities. Intensities are then centered by substracting the median of the ratios for each sample.



0 50 100 150 200 0 2 4 6 10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 Count Frenquency (%) Missing values distribution accross samples Save figure
0 500 1000 1500 2000 0 20 40 60 80 0 10 20 30 40 Number of NA values Number of proteins Frenquency (%) Missing values distribution accross proteins Save figure


0 40000 80000 120000 6 8 10 log(intensity) count imputed FALSE TRUE Log intensities distribution with imputed values Save figure

Missing values are imputed with the gaussian model implemented in the library.



96% 1.9% 0.2% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0.1% 0 25 50 75 100 1 2 3 4 5 6 7 8 9 10 Dimensions Percentage of explained variances Inertia Save figure
0 5 -20 -10 0 10 Axis1 Axis2 0 10 20 30 Missing_values Projection of proteins Save figure


10amol_1_norm 10amol_2_norm 10amol_3_norm 10amol_4_norm 50amol_1_norm 50amol_3_norm 50amol_2_norm 50amol_4_norm 100amol_1_norm 100amol_3_norm 100amol_2_norm 100amol_4_norm 250amol_1_norm 250amol_2_norm 250amol_3_norm 250amol_4_norm 500amol_1_norm 500amol_3_norm 500amol_2_norm 500amol_4_norm 1fmol_1_norm 1fmol_2_norm 1fmol_3_norm 1fmol_4_norm 5fmol_1_norm 5fmol_3_norm 5fmol_2_norm 5fmol_4_norm 10fmol_1_norm 10fmol_2_norm 10fmol_3_norm 10fmol_4_norm 25fmol_1_norm 25fmol_2_norm 25fmol_3_norm 25fmol_4_norm 50fmol_1_norm 50fmol_2_norm 50fmol_3_norm 50fmol_4_norm -1.0 -0.5 0.0 0.5 1.0 -1.0 -0.5 0.0 0.5 1.0 Dim1 (96%) Dim2 (1.9%) 2.488 2.492 2.496 2.500 2.504 contrib Samples contribution Save figure
10amol_1 10amol_2 10amol_3 10amol_4 50amol_1 50amol_3 50amol_2 50amol_4 100amol_1 100amol_3 100amol_2 100amol_4 250amol_1 250amol_2 250amol_3 250amol_4 500amol_1 500amol_3 500amol_2 500amol_4 1fmol_1 1fmol_2 1fmol_3 1fmol_4 5fmol_1 5fmol_3 5fmol_2 5fmol_4 10fmol_1 10fmol_2 10fmol_3 10fmol_4 25fmol_1 25fmol_2 25fmol_3 25fmol_4 50fmol_1 50fmol_2 50fmol_3 50fmol_4 -0.1 0.0 0.1 0.2 -1.00 -0.75 -0.50 -0.25 0.00 PC1 [96%] PC2 [2%] Samples projection Save figure


500amol_2 1fmol_2 500amol_1 1fmol_1 500amol_3 1fmol_3 500amol_4 1fmol_4 10amol_3 250amol_4 50amol_4 10amol_4 100amol_4 10amol_1 50amol_1 100amol_1 250amol_1 250amol_3 50amol_3 100amol_3 50amol_2 250amol_2 10amol_2 100amol_2 50fmol_4 50fmol_1 50fmol_2 50fmol_3 25fmol_2 25fmol_3 5fmol_4 5fmol_3 10fmol_3 5fmol_1 5fmol_2 10fmol_4 25fmol_4 25fmol_1 10fmol_1 10fmol_2 Sample Protein 5 6 7 8 9 log_intensity Save figure